Antimicrobial resistance is one of the greatest threats to human health worldwide and carbapenem-resistant enterobacteriaceae (CRE) represent an immediate public health threat that requires urgent and aggressive action. In the US, infections caused by resistant organisms add $21-$34 billion to healthcare costs annually. Carbapenem-resistant Klebsiella pneumoniae (CRKP) are the most commonly encountered CRE in the US. CRKP are resistant to most antibiotics and clinical outcomes with CRKP infections are generally poor. The globally endemic CRKP strain ST258 is responsible for most CRKP infections in the US. The overarching hypothesis of this R21 proposal is that ST258 strains of CRKP carry specific genes that are associated with poor clinical outcomes and that these genetic elements are nonuniformly distributed among the isolates. Using whole genome sequencing we will seek to identify genetic and clinical markers of poor outcomes and transmissibility by comparison of colonizing isolates versus those that cause infection. We have already determined that ST258 strains from the Great Lakes region can be grouped based on the presence of two plasmids carrying the blaKPC gene. In addition, the two plasmids are associated with distinct chromosomal backgrounds that differ in many genes including those that encode the capsular polysaccharide structure. Finding the links between these observations will help stratify at risk patients by determining which CRKP isolates and what genetic signatures have the most clinical impact. To obtain these answers, we will join our established multicenter CRKP consortium, which currently consists of 9 hospital systems, covering more than 2 million people living in the Great Lakes region with the genomics expertise of JCVI. Since January of 2012, more than 500 unique patients with greater than 750 admissions and over 850 CRKP culture episodes have been included in this consortium; so far, we have analyzed 57 strains by WGS. We have 2 specific aims. 1) To discover molecular characteristics that are associated with clinical outcomes in patients infected with ST258 strains of CRKP. We will determine the genomic sequences of CRKP isolates collected from patients with extensive clinical information, treatment history, and outcome data. The primary outcome of interest will be association of genetic variants with hospital mortality. Secondary measures will include variants associated with post-infection length of stay, ICU admission, and readmissions. 2) To study the interplay between clinical risk factors and molecular characteristics leading to tigecycline and colistin resistance in CRKP isolates. We will determine the mechanisms of resistance of strains with reduced in vitro susceptibility to tigecycline and/or colistin and whethr specific genetic backgrounds in the context of specific clinical settings - such as antibiotic exposure or stay in long term care - are associated with tigecycline and/or colistin resistance. Molecular results combined with clinical/epidemiologic data will inform these models. Our unique approach will provide the necessary understanding that is crucial in the design of interventions to curb the CRKP epidemic.